globaldata.cpp

   1 #include <iostream>
   2 #include <iomanip>
   3 #include <string>
   4 #include <map>
   5 #include <sstream>
   6 #include <stdexcept>
   7
   8 using namespace std;
   9
  10 #include "globaldata.hpp"
  11 #include "sparsematrix.hpp"
  12 #include "rabundvector.hpp"
  13 #include "sabundvector.hpp"
  14 #include "listvector.hpp"
  15 #include <exception>
  16 #include <iostream>
  17
  18 /*******************************************************/
  19
  20 /******************************************************/
  21 GlobalData* GlobalData::getInstance() {
  22         if( _uniqueInstance == 0 ) {
  23                 _uniqueInstance = new GlobalData();
  24         }
  25         return _uniqueInstance;
  26 }
  27 /*******************************************************/
  28
  29 /******************************************************/
  30
  31 ListVector* GlobalData::getListVector()         {       return gListVector;             }
  32 /*******************************************************/
  33
  34 /******************************************************/
  35 void GlobalData::setListVector(ListVector* lv){
  36         try {
  37                 if(gListVector != NULL){        delete gListVector;     }
  38                 gListVector = new ListVector(*lv);
  39         }
  40         catch(exception& e) {
  41                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  42                 exit(1);
  43         }
  44         catch(...) {
  45                 cout << "An unknown error has occurred in the GlobalData class function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  46                 exit(1);
  47         }
  48 }
  49
  50 /*******************************************************/
  51
  52 /******************************************************/
  53
  54 SparseMatrix* GlobalData::getSparseMatrix()     {       return gSparseMatrix;   }
  55 /*******************************************************/
  56
  57 /******************************************************/
  58 void GlobalData::setSparseMatrix(SparseMatrix* sm){
  59         try{
  60                 if(gSparseMatrix != NULL){      delete gSparseMatrix;   }
  61                 gSparseMatrix = new SparseMatrix(*sm);
  62         }
  63         catch(exception& e) {
  64                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  65                 exit(1);
  66         }
  67         catch(...) {
  68                 cout << "An unknown error has occurred in the GlobalData class function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  69                 exit(1);
  70         }
  71
  72 }
  73 /*******************************************************/
  74
  75 /******************************************************/
  76 //This function parses through the option string of the command to remove its parameters
  77 void GlobalData::parseGlobalData(string commandString, string optionText){
  78         try {
  79                 allLines = 1;
  80                 commandName = commandString; //save command name to be used by other classes
  81
  82                 //clears out data from previous read
  83                 if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.list")) {
  84                         clear();
  85                 }
  86
  87                 //saves help request
  88                 if (commandName =="help") {
  89                         helpRequest = optionText;
  90                 }
  91
  92                 string key, value;
  93                 //reads in parameters and values
  94                 if((optionText != "") && (commandName != "help")){
  95                         while((optionText.find_first_of(',') != -1)) {  //while there are parameters
  96                                 splitAtComma(value, optionText);
  97                                 splitAtEquals(key, value);
  98
  99                                 if (key == "phylipfile" )       { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
 100                                 if (key == "columnfile" )       { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
 101                                 if (key == "listfile" )         { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
 102                                 if (key == "rabundfile" )       { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
 103                                 if (key == "sabundfile" )       { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
 104                                 if (key == "fastafile" )        { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 105                                 if (key == "namefile" )         { namefile = value;             }
 106                                 if (key == "orderfile" )        { orderfile = value;    }
 107                                 if (key == "groupfile" )        { groupfile = value;    }
 108                                 if (key == "cutoff" )           { cutoff = value;               }
 109                                 if (key == "precision" )        { precision = value;    }
 110                                 if (key == "iters" )            { iters = value;                }
 111                                 if (key == "jumble" )           { jumble = value;               }
 112                                 if (key == "freq" )                     { freq = value;                 }
 113                                 if (key == "method" )           { method = value;               }
 114                                 if (key == "fileroot" )         { fileroot = value;             }
 115
 116                                 if (key == "single") {//stores estimators in a vector
 117                                         singleEstimators.clear(); //clears out old values
 118                                         if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; }
 119                                         splitAtDash(value, singleEstimators);
 120                                 }
 121                                 if (key == "rarefaction") {//stores estimators in a vector
 122                                         rareEstimators.clear(); //clears out old values
 123                                         if (value == "default") { value = "rarefraction"; }
 124                                         splitAtDash(value, rareEstimators);
 125                                 }
 126                                 if (key == "shared") {//stores estimators in a vector
 127                                         sharedEstimators.clear(); //clears out old values
 128                                         if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 129                                         splitAtDash(value, sharedEstimators);
 130                                 }
 131                                 if (key == "summary") { //stores summaries to be used in a vector
 132                                         summaryEstimators.clear();
 133                                         if (value == "default") { value = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 134                                         splitAtDash(value, summaryEstimators);
 135                                 }
 136                                 if (key == "sharedsummary") { //stores sharedSummaries to be used in a vector
 137                                         sharedSummaryEstimators.clear();
 138                                         if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 139                                         splitAtDash(value, sharedSummaryEstimators);
 140                                 }
 141                                 if (key == "sharedrarefaction") { //stores sharedrarefaction to be used in a vector
 142                                         sharedRareEstimators.clear();
 143                                         if (value == "default") { value = "sharedobserved"; }
 144                                         splitAtDash(value, sharedRareEstimators);
 145                                 }
 146                                 if (key == "line") {//stores lines to be used in a vector
 147                                         lines.clear();
 148                                         line = value;
 149                                         splitAtDash(value, lines);
 150                                         allLines = 0;
 151                                 }
 152                                 if (key == "label") {//stores lines to be used in a vector
 153                                         labels.clear();
 154                                         label = value;
 155                                         splitAtDash(value, labels);
 156                                         allLines = 0;
 157                                 }
 158                         }
 159
 160                         //saves the last parameter
 161                         value = optionText;
 162                         splitAtEquals(key, value);
 163                         if (key == "phylipfile" )       { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip";       }
 164                         if (key == "columnfile" )       { columnfile = value; inputFileName = value; fileroot = value; format = "column";       }
 165                         if (key == "listfile" )         { listfile = value; inputFileName = value; fileroot = value; format = "list";           }
 166                         if (key == "rabundfile" )       { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund";       }
 167                         if (key == "sabundfile" )       { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund";       }
 168                         if (key == "fastafile" )        { fastafile = value; inputFileName = value; fileroot = value; format = "fasta";         }
 169                         if (key == "namefile" )         { namefile = value;             }
 170                         if (key == "orderfile" )        { orderfile = value;    }
 171                         if (key == "groupfile" )        { groupfile = value;    }
 172                         if (key == "cutoff" )           { cutoff = value;               }
 173                         if (key == "precision" )        { precision = value;    }
 174                         if (key == "iters" )            { iters = value;                }
 175                         if (key == "jumble" )           { jumble = value;               }
 176                         if (key == "freq" )                     { freq = value;                 }
 177                         if (key == "method" )           { method = value;               }
 178                         if (key == "fileroot" )         { fileroot = value;             }
 179
 180                         if (key == "single") {//stores estimators in a vector
 181                                 singleEstimators.clear(); //clears out old values
 182                                 if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; }
 183                                 splitAtDash(value, singleEstimators);
 184                         }
 185                         if (key == "rarefaction") {//stores estimators in a vector
 186                                 rareEstimators.clear(); //clears out old values
 187                                 if (value == "default") { value = "rarefraction"; }
 188                                 splitAtDash(value, rareEstimators);
 189                         }
 190                         if (key == "shared") {//stores estimators in a vector
 191                                 sharedEstimators.clear(); //clears out old values
 192                                 if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 193                                 splitAtDash(value, sharedEstimators);
 194                         }
 195                         if (key == "summary") { //stores summaries to be used in a vector
 196                                 summaryEstimators.clear();
 197                                 if (value == "default") { value = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; }
 198                                 splitAtDash(value, summaryEstimators);
 199                         }
 200                         if (key == "sharedsummary") { //stores sharedSummaries to be used in a vector
 201                                 sharedSummaryEstimators.clear();
 202                                 if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; }
 203                                 splitAtDash(value, sharedSummaryEstimators);
 204                         }
 205                         if (key == "sharedrarefaction") { //stores sharedrarefaction to be used in a vector
 206                                 sharedRareEstimators.clear();
 207                                 if (value == "default") { value = "sharedobserved"; }
 208                                 splitAtDash(value, sharedRareEstimators);
 209                         }
 210
 211                         if (key == "line") {//stores lines to be used in a vector
 212                                 lines.clear();
 213                                 line = value;
 214                                 splitAtDash(value, lines);
 215                                 allLines = 0;
 216                         }
 217                         if (key == "label") {//stores lines to be used in a vector
 218                                 labels.clear();
 219                                 label = value;
 220                                 splitAtDash(value, labels);
 221                                 allLines = 0;
 222                         }
 223                 }
 224
 225                 //set format for shared
 226                 if ((listfile != "") && (groupfile != "")) { format = "shared"; }
 227
 228                 //input defaults
 229                 if (commandString == "collect.single") {
 230                         if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); }
 231                 }
 232                 if (commandString == "rarefaction.single") {
 233                         if (rareEstimators.size() == 0) { splitAtDash(rarefaction, rareEstimators);  }
 234                 }
 235                 if (commandString == "collect.shared") {
 236                         if (sharedEstimators.size() == 0) { splitAtDash(shared, sharedEstimators); }
 237                 }
 238                 if (commandString == "summary.single") {
 239                         if (summaryEstimators.size() == 0) { splitAtDash(summary, summaryEstimators); }
 240                 }
 241                 if (commandString == "summary.shared") {
 242                         if (sharedSummaryEstimators.size() == 0) { splitAtDash(sharedsummary, sharedSummaryEstimators); }
 243                 }
 244                 if (commandString == "rarefaction.shared") {
 245                         if (sharedRareEstimators.size() == 0) { splitAtDash(sharedrarefaction, sharedRareEstimators); }
 246                 }
 247
 248
 249         }
 250         catch(exception& e) {
 251                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 252                 exit(1);
 253         }
 254         catch(...) {
 255                 cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 256                 exit(1);
 257         }
 258
 259 }
 260 /*******************************************************/
 261
 262 /******************************************************/
 263 // These functions give you the option parameters of the commands
 264 string GlobalData::getPhylipFile()              {       return phylipfile;      }
 265 string GlobalData::getColumnFile()              {       return columnfile;      }
 266 string GlobalData::getListFile()                {       return listfile;        }
 267 string GlobalData::getRabundFile()              {       return rabundfile;      }
 268 string GlobalData::getSabundFile()              {       return sabundfile;      }
 269 string GlobalData::getNameFile()                {       return namefile;        }
 270 string GlobalData::getGroupFile()               {       return groupfile;       }
 271 string GlobalData::getOrderFile()               {       return orderfile;       }
 272 string GlobalData::getFastaFile()               {       return fastafile;       }
 273 string GlobalData::getCutOff()                  {       return cutoff;          }
 274 string GlobalData::getFormat()                  {       return format;          }
 275 string GlobalData::getPrecision()               {       return precision;       }
 276 string GlobalData::getMethod()                  {       return method;          }
 277 string GlobalData::getFileRoot()                {       return fileroot;        }
 278 string GlobalData::getIters()                   {       return iters;           }
 279 string GlobalData::getJumble()                  {       return jumble;          }
 280 string GlobalData::getFreq()                    {       return freq;            }
 281 void GlobalData::setListFile(string file)       {       listfile = file;        inputFileName = file;}
 282 void GlobalData::setRabundFile(string file)     {       rabundfile = file;      inputFileName = file;}
 283 void GlobalData::setSabundFile(string file)     {       sabundfile = file;      inputFileName = file;}
 284 void GlobalData::setPhylipFile(string file)     {       phylipfile = file;    inputFileName = file;}
 285 void GlobalData::setColumnFile(string file)     {       columnfile = file;    inputFileName = file;}
 286 //void GlobalData::setGroupFile(string file)    {       groupfile = file;       }
 287 void GlobalData::setNameFile(string file)       {       namefile = file;        }
 288 void GlobalData::setFormat(string Format)       {       format = Format;        }
 289
 290
 291 /*******************************************************/
 292
 293 /******************************************************/
 294
 295 GlobalData::GlobalData() {
 296         //option definitions should go here...
 297         helpRequest = "";
 298         clear();
 299 }
 300 /*******************************************************/
 301
 302 /******************************************************/
 303
 304 void GlobalData::clear() {
 305         //option definitions should go here...
 306         phylipfile              =       "";
 307         columnfile              =       "";
 308         listfile                =       "";
 309         rabundfile              =       "";
 310         sabundfile              =       "";
 311         namefile                =       "";
 312         groupfile               =       "";
 313         orderfile               =       "";
 314         fastafile               =   "";
 315         cutoff                  =       "10.00";
 316         format                  =       "";
 317         precision               =       "100";
 318         iters                   =       "1000";
 319         line                    =   "";
 320         label                   =       "";
 321         jumble                  =       "0";
 322         freq                    =       "100";
 323         method                  =       "furthest";
 324         fileroot                =       "";
 325         single                  =       "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction";
 326         rarefaction             =       "rarefaction";
 327         shared                  =       "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
 328         sharedsummary   =   "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN";
 329         summary                 =       "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson";
 330         sharedrarefaction = "sharedobserved";
 331 }
 332 /*******************************************************/
 333
 334 /******************************************************/
 335
 336 GlobalData::~GlobalData() {
 337         _uniqueInstance = 0;
 338         if(gListVector != NULL)         {       delete gListVector;             }
 339         if(gSparseMatrix != NULL)       {       delete gSparseMatrix;   }
 340         if(gorder != NULL)                      {       delete gorder;          }
 341 }
 342 /*******************************************************/
 343
 344 /******************************************************/
 345 //This function parses the estimator options and puts them in a vector
 346 void GlobalData::splitAtDash(string& estim, vector<string>& container) {
 347         try {
 348                 string individual;
 349
 350                 while (estim.find_first_of('-') != -1) {
 351                         individual = estim.substr(0,estim.find_first_of('-'));
 352                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 353                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 354                                 container.push_back(individual);
 355                         }
 356                 }
 357                 //get last one
 358                 container.push_back(estim);
 359         }
 360         catch(exception& e) {
 361                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 362                 exit(1);
 363         }
 364         catch(...) {
 365                 cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 366                 exit(1);
 367         }
 368
 369 }
 370 /*******************************************************/
 371
 372 /******************************************************/
 373 //This function parses the label options and puts them in a set
 374 void GlobalData::splitAtDash(string& estim, set<string>& container) {
 375         try {
 376                 string individual;
 377
 378                 while (estim.find_first_of('-') != -1) {
 379                         individual = estim.substr(0,estim.find_first_of('-'));
 380                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 381                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 382                                 container.insert(individual);
 383                         }
 384                 }
 385                 //get last one
 386                 container.insert(estim);
 387         }
 388         catch(exception& e) {
 389                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 390                 exit(1);
 391         }
 392         catch(...) {
 393                 cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 394                 exit(1);
 395         }
 396
 397 }
 398 /*******************************************************/
 399
 400 /******************************************************/
 401 //This function parses the line options and puts them in a set
 402 void GlobalData::splitAtDash(string& estim, set<int>& container) {
 403         try {
 404                 string individual;
 405                 int lineNum;
 406
 407                 while (estim.find_first_of('-') != -1) {
 408                         individual = estim.substr(0,estim.find_first_of('-'));
 409                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 410                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 411                                 convert(individual, lineNum); //convert the string to int
 412                                 container.insert(lineNum);
 413                         }
 414                 }
 415                 //get last one
 416                 convert(estim, lineNum); //convert the string to int
 417                 container.insert(lineNum);
 418         }
 419         catch(exception& e) {
 420                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 421                 exit(1);
 422         }
 423         catch(...) {
 424                 cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 425                 exit(1);
 426         }
 427
 428 }
 429 /*******************************************************/
 430
 431 /******************************************************/
 432
 433 //This function splits up the various option parameters
 434 void GlobalData::splitAtComma(string& prefix, string& suffix){
 435         try {
 436                 prefix = suffix.substr(0,suffix.find_first_of(','));
 437                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
 438                         suffix = suffix.substr(suffix.find_first_of(',')+2, suffix.length());
 439                 }
 440         }
 441         catch(exception& e) {
 442                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 443                 exit(1);
 444         }
 445         catch(...) {
 446                 cout << "An unknown error has occurred in the GlobalData class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 447                 exit(1);
 448         }
 449
 450 }
 451 /*******************************************************/
 452
 453 /******************************************************/
 454 //This function separates the key value from the option value i.e. distfile = "96_..."
 455 void GlobalData::splitAtEquals(string& key, string& value){
 456         try {
 457                 if(value.find_first_of('=') != -1){
 458                         key = value.substr(0,value.find_first_of('='));
 459                         if ((value.find_first_of('=')+1) <= value.length()) {
 460                                 value = value.substr(value.find_first_of('=')+1, value.length());
 461                         }
 462                 }else{
 463                         key = value;
 464                         value = 1;
 465                 }
 466         }
 467         catch(exception& e) {
 468                 cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 469                 exit(1);
 470         }
 471         catch(...) {
 472                 cout << "An unknown error has occurred in the GlobalData class function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 473                 exit(1);
 474         }
 475
 476 }
 477 /*******************************************************/
 478
 479 /******************************************************/